Increased accuracy of starch granule type quantification using mixture distributions

Background: The proportion of granule types in wheat starch is an important characteristic that can affect its functionality. It is widely accepted that granule types are either large, disc-shaped A-type granules or small, spherical B-type granules. Additionally, there are some reports of the tiny C-type granules. The differences between these granule types are due to its carbohydrate composition and crystallinity which is highly, but not perfectly, correlated with the granule size. A majority of the studies that have considered granule types analyse them based on a size threshold rather than chemical composition. This is understandable due to the expense of separating starch into different types. While the use of a size threshold to classify granule type is a low-cost measure, this results in misclassification. We present an alternative, statistical method to quantify the proportion of granule types by a fit of the mixture distribution, along with an R package, a web based app and a video tutorial for how to use the web app to enable its straightforward application. Results: Our results show that the reliability of the gen otypic effects increase approximately 60% using the proportions of the A-type and B-type granule estimated by the mixture distribution over the standard size-threshold measure. Although there was a marginal drop in reliability for C-type granules. The latter is likely due to the low observed genetic variance for C-type granules. Conclusions: The determination of the proportion of granule types from size-distribution is better achieved by using the mixing probabilities from the fit of the mixture distribution rather than using a size-threshold

Bond-rearrangement and ionization mechanisms in the photo-double-ionization of simple hydrocarbons (C2H4, C2H3F, and 1,1-C2H2F2) near and above threshold

Citation: Gaire, B., Gatton, A., Wiegandt, F., Neff, J., Janke, C., Zeller, S., . . . Weber, T. (2016). Bond-rearrangement and ionization mechanisms in the photo-double-ionization of simple hydrocarbons (C2H4, C2H3F, and 1,1-C2H2F2) near and above threshold. Physical Review A, 94(3), 8. doi:10.1103/PhysRevA.94.033412We investigate bond-rearrangement driven by photo-double-ionization (PDI) near and above the double-ionization threshold in a sequence of carbon-carbon double-bonded hydrocarbon molecules: ethylene, fluoroethylene, and 1,1-difluoroethylene. We employ the kinematically complete cold target recoil ion momentum spectroscopy method to resolve all photo-double-ionization events leading to two-ion fragments. We observe changes in the branching ratios of different dissociative ionization channels depending on the presence of no, one, or two fluorine atoms. The role of the fluorine atom in the bond-rearrangement channels is intriguing, as evident by the reordering of the threshold energies of the PDI in the fluorinated molecules. These effects offer a compelling argument that the electronegativity of the fluorine (or the polarity of the molecule) strongly influences the potential energy surfaces of the molecules and drives bond rearrangement during the dissociation process. The energy sharing and the relative angle between the three-dimensional momentum vectors of the two electrons enable us to distinguish between knockout and other ionization mechanisms of the PDI processes

Adaptive strong-field control of chemical dynamics guided by three-dimensional momentum imaging.

Shaping ultrafast laser pulses using adaptive feedback can manipulate dynamics in molecular systems, but extracting information from the optimized pulse remains difficult. Experimental time constraints often limit feedback to a single observable, complicating efforts to decipher the underlying mechanisms and parameterize the search process. Here we show, using two strong-field examples, that by rapidly inverting velocity map images of ions to recover the three-dimensional photofragment momentum distribution and incorporating that feedback into the control loop, the specificity of the control objective is markedly increased. First, the complex angular distribution of fragment ions from the nω+C2D4→C2D3++D interaction is manipulated. Second, isomerization of acetylene (nω+C2H2→C2H22+→CH2++C+) is controlled via a barrier-suppression mechanism, a result that is validated by model calculations. Collectively, these experiments comprise a significant advance towards the fundamental goal of actively guiding population to a specified quantum state of a molecule

Auger decay and subsequent fragmentation pathways of ethylene following K-shell ionization

Citation: Gaire, B., Haxton, D. J., Sturm, F. P., Williams, J., Gatton, A., Bocharova, I., . . . Weber, T. (2015). Auger decay and subsequent fragmentation pathways of ethylene following K-shell ionization. Physical Review A, 92(1), 13. doi:10.1103/PhysRevA.92.013408The fragmentation pathways and dynamics of ethylene molecules after core ionization are explored using coincident measurements of the Auger electron and fragment ions by employing the cold target recoil-ion momentum spectroscopy method. The influence of several factors on the dynamics and kinematics of the dissociation is studied. These include propensity rules, ionization mechanisms, symmetry of the orbitals from which the Auger electrons originate, multiple scattering, conical intersections, interference, and possible core-hole localization for the double ionization of this polyatomic molecule. Energy correlation maps allow probing the multidimensional potential energy surfaces and, in combination with our multiconfiguration self-consistent field calculations, identifying the populated electronic states of the dissociating dication. The measured angular distributions of the Auger electrons in the molecular frame further support and augment these assignments. The deprotonation and molecular hydrogen ion elimination channels show a nearly isotropic Auger electron angular distribution with a small elongation along the direction perpendicular to the molecular axis. For the symmetric breakup the angular distributions show a clear influence of multiple scattering on the outgoing electrons. The lowest kinetic energy release feature of the symmetric breakup channel displays a fingerprint of entangled Auger and photoelectron motion in the angular emission pattern identifying this transition as an excellent candidate to probe core-hole localization at a conical intersection of a polyatomic molecule.Additional Authors: Landers, A. L.;Belkacem, A.;Dorner, R.;Weber, T

Ultrafast temporal evolution of interatomic Coulombic decay in NeKr dimers

We investigate interatomic Coulombic decay in NeKr dimers after neon inner-valence photoionization [Ne+(2s-1)] using a synchrotron light source. We measure with high energy resolution the two singly charged ions of the Coulomb-exploding dimer dication and the photoelectron in coincidence. By carefully tracing the post-collision interaction between the photoelectron and the emitted ICD electron we are able to probe the temporal evolution of the state as it decays. Although the ionizing light pulses are 80 picoseconds long, we determine the lifetime of the intermediate dimer cation state and visualize the contraction of the nuclear structure on the femtosecond time scale

Hydrogen and fluorine migration in photo-double-ionization of 1,1-difluoroethylene (1,1-C2H2F2) near and above threshold

We have studied the nondissociative and dissociative photo-double-ionization of 1,1-difluoroethylene using single photons of energies ranging from 40 to 70 eV. Applying a coincident electron-ion three-dimensional momentum imaging technique, kinematically complete measurements have been achieved. We present the branching ratios of the six reaction channels identified in the experiment. Electron-ion energy maps and relative electron emission angles are used to distinguish between direct and indirect photo-double-ionization mechanisms at a few different photon energies. The influence of selection and propensity rules is discussed. Threshold energies of double ionization are extracted from the sum of the kinetic energies of the electrons, which hint to the involvement of different manifolds of states. The dissociative ionization channels with two ionic fragments are explored in detail by measuring the kinetic energy release of the fragment ions, sum of the kinetic energies, as well as the energy sharing of the two emitted electrons. We investigate the migration of hydrogen and fluorine atoms and compare the experimental results to the photo-double-ionization of centrosymmetric linear and planar hydrocarbons (C[subscript 2]H[subscript 2] and C[subscript 2]H[subscript 4]) whenever possible

Incorporating real time velocity map image reconstruction into closed-loop coherent control

We report techniques developed to utilize three-dimensional momentum information as feedback in adaptive femtosecond control of molecular dynamics. Velocity map imaging is used to obtain the three-dimensional momentum map of the dissociating ions following interaction with a shaped intense ultrafast laser pulse. In order to recover robust feedback information, however, the two-dimensional momentum projection from the detector must be inverted to reconstruct the full three-dimensional momentum of the photofragments. These methods are typically slow or require manual inputs and are therefore accomplished offline after the images have been obtained. Using an algorithm based upon an “onion-peeling” (also known as “back projection”) method, we are able to invert 1040 × 1054 pixel images in under 1 s. This rapid inversion allows the full photofragment momentum to be used as feedback in a closed-loop adaptive control scheme, in which a genetic algorithm tailors an ultrafast laser pulse to optimize a specific outcome. Examples of three-dimensional velocity map image based control applied to strong-field dissociation of CO and O2 are presented

Strong-field dissociation dynamics of molecular dications

Citation: Jochim, B., Severt, T., Zohrabi, M., Ablikim, U., Berry, B., Gaire, B., . . . Ben-Itzhak, I. (2015). Strong-field dissociation dynamics of molecular dications. 635(11). doi:10.1088/1742-6596/635/11/112044We focus on the dissociation of metastable molecular dications induced by intense, ultrafast laser pulses. In particular, we demonstrate the dominant role of commonly-neglected permanent-dipole transitions and drive dissociation via a pump-dump-like mechanism within a single laser pulse. © Published under licence by IOP Publishing Ltd

Application of a risk-management framework for integration of stromal tumor-infiltrating lymphocytes in clinical trials

Stromal tumor-infiltrating lymphocytes (sTILs) are a potential predictive biomarker for immunotherapy response in metastatic triple-negative breast cancer (TNBC). To incorporate sTILs into clinical trials and diagnostics, reliable assessment is essential. In this review, we propose a new concept, namely the implementation of a risk-management framework that enables the use of sTILs as a stratification factor in clinical trials. We present the design of a biomarker risk-mitigation workflow that can be applied to any biomarker incorporation in clinical trials. We demonstrate the implementation of this concept using sTILs as an integral biomarker in a single-center phase II immunotherapy trial for metastatic TNBC (TONIC trial, NCT02499367), using this workflow to mitigate risks of suboptimal inclusion of sTILs in this specific trial. In this review, we demonstrate that a web-based scoring platform can mitigate potential risk factors when including sTILs in clinical trials, and we argue that this framework can be applied for any future biomarker-driven clinical trial setting

A Family of Plasmodesmal Proteins with Receptor-Like Properties for Plant Viral Movement Proteins

Plasmodesmata (PD) are essential but poorly understood structures in plant cell walls that provide symplastic continuity and intercellular communication pathways between adjacent cells and thus play fundamental roles in development and pathogenesis. Viruses encode movement proteins (MPs) that modify these tightly regulated pores to facilitate their spread from cell to cell. The most striking of these modifications is observed for groups of viruses whose MPs form tubules that assemble in PDs and through which virions are transported to neighbouring cells. The nature of the molecular interactions between viral MPs and PD components and their role in viral movement has remained essentially unknown. Here, we show that the family of PD-located proteins (PDLPs) promotes the movement of viruses that use tubule-guided movement by interacting redundantly with tubule-forming MPs within PDs. Genetic disruption of this interaction leads to reduced tubule formation, delayed infection and attenuated symptoms. Our results implicate PDLPs as PD proteins with receptor-like properties involved the assembly of viral MPs into tubules to promote viral movement